Thanks to both of you for the stories and the tips!
I'm going to try to clean the digging pit/den this weekend. I'm hoping to just find the source of the ammonia smell and leave as much of the substrate and tunnels intact as possible. It's not weird to smell different parts of your hamsters bedding, right?
I'm going to try a bigger/darker housing over it too and the sand pit. I think his prior options didn't get dark enough, now that i'm looking at it. He does seem to hate light. Or just us. He seems to want to wake up when we go to sleep, and go to sleep when we wake up. Although sometimes he'll just want to play and play, and other times like he's never met me before. More questions about this.. I think I'm supposed to start a new thread for a slightly different topic though?
I'll keep you posted on how it goes!